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Augustus PPX: Invalid block no. in SubstateModel::blockNoOfB

Posted: Wed Apr 13, 2016 4:30 pm
by lkremer
Hello everyone,

I'm trying to use AUGUSTUS in conjunction with your protein profile
extension to improve the annotation of several gene families. In many
cases, AUGUSTUS runs as expected and gives me useful hits based on the
protein profile I specified.

However, in some cases I receive this error message:

../augustus/bin/augustus: ERROR
Invalid block no. in SubstateModel::blockNoOfB

The command I'm using is:

augustus --species=fly scaffold1499.fa --proteinprofile=all_but_Mnat_16289.prfl

If I run AUGUSTUS without specifying a protein profile, AUGUSTUS runs as
expected and prints a GFF containing several genes.

I generated the protein profile using this command: --qij=augustus/config/profile/blosum62.qij all_but_Mnat_16289_aln.fa > all_but_Mnat_16289.prfl

None of the input files are empty, and the MSA looks reasonable.

The scaffold I'm annotating is rather small and contains several unknown
nucleotides, maybe this causes problems with the PPX. Augustus without
the protein profile option does not crash, however. And the exact same
approach works for me when using other genes/scaffolds.

I'd be very grateful if you could help me with this problem. If you need
more information or files, let me know and I will provide them to you.
I tried contacting Oliver Keller but his email does not seem to work.

Thank you in advance!

Full output of the error:
# This output was generated with AUGUSTUS (version 3.2.2).
# AUGUSTUS is a gene prediction tool written by M. Stanke
# O. Keller, S. K├Ânig, L. Gerischer and L. Romoth.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David
Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de
novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters using config directory
/global/public/home/l_krem02/tools/augustus/config/ ...
# Using protein profile unknown
# --[0..295]--> unknown_A (54) <--[0..3]--> unknown_B (51) <--[0..6]-->
unknown_C (11) <--[1..253]--
# fly version. Using default transition matrix.
# Looks like scaffold1499.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
# ----- prediction on sequence number 1 (length = 139837, name =
scaffold1499) -----
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands

../augustus/bin/augustus: ERROR
Invalid block no. in SubstateModel::blockNoOfB

Re: Augustus PPX: Invalid block no. in SubstateModel::blockNoOfB

Posted: Mon May 01, 2017 7:56 pm
by lassancejm
Did you ever find what was causing this error?

I have encountered the same error message with the ppx extension, but I am still uncertain about what the cause actually is.


Re: Augustus PPX: Invalid block no. in SubstateModel::blockNoOfB

Posted: Mon Jan 29, 2018 9:08 am
by katharina
No, Mario had no time to look into this, yet. Sorry.